Magnesium in PDB 7lq0: Crystal Structures and Ribonuclease Activity of the Flavivirus Host Factor ERI3 That Is Involved in Viral Rna Synthesis Define the Eri Subfamily of Structure-Specific 3-Prime - 5-Prime Exoribonucleases
Protein crystallography data
The structure of Crystal Structures and Ribonuclease Activity of the Flavivirus Host Factor ERI3 That Is Involved in Viral Rna Synthesis Define the Eri Subfamily of Structure-Specific 3-Prime - 5-Prime Exoribonucleases, PDB code: 7lq0
was solved by
R.Thapar,
A.S.Andrew,
J.A.Tainer,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
37.23 /
1.60
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
58.529,
74.2,
96.487,
90,
90,
90
|
R / Rfree (%)
|
16.2 /
19.9
|
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Crystal Structures and Ribonuclease Activity of the Flavivirus Host Factor ERI3 That Is Involved in Viral Rna Synthesis Define the Eri Subfamily of Structure-Specific 3-Prime - 5-Prime Exoribonucleases
(pdb code 7lq0). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the
Crystal Structures and Ribonuclease Activity of the Flavivirus Host Factor ERI3 That Is Involved in Viral Rna Synthesis Define the Eri Subfamily of Structure-Specific 3-Prime - 5-Prime Exoribonucleases, PDB code: 7lq0:
Jump to Magnesium binding site number:
1;
2;
3;
4;
Magnesium binding site 1 out
of 4 in 7lq0
Go back to
Magnesium Binding Sites List in 7lq0
Magnesium binding site 1 out
of 4 in the Crystal Structures and Ribonuclease Activity of the Flavivirus Host Factor ERI3 That Is Involved in Viral Rna Synthesis Define the Eri Subfamily of Structure-Specific 3-Prime - 5-Prime Exoribonucleases
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Crystal Structures and Ribonuclease Activity of the Flavivirus Host Factor ERI3 That Is Involved in Viral Rna Synthesis Define the Eri Subfamily of Structure-Specific 3-Prime - 5-Prime Exoribonucleases within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg502
b:34.1
occ:1.00
|
O1P
|
A:AMP501
|
2.0
|
34.2
|
1.0
|
O
|
A:HOH628
|
2.1
|
37.9
|
1.0
|
O
|
A:HOH679
|
2.1
|
35.3
|
1.0
|
O
|
A:HOH605
|
2.1
|
37.1
|
1.0
|
O
|
A:HOH637
|
2.1
|
32.7
|
1.0
|
OD2
|
A:ASP150
|
2.1
|
34.6
|
1.0
|
CG
|
A:ASP150
|
3.1
|
34.7
|
1.0
|
P
|
A:AMP501
|
3.3
|
34.5
|
1.0
|
OD1
|
A:ASP150
|
3.4
|
36.1
|
1.0
|
MG
|
A:MG503
|
3.4
|
45.9
|
1.0
|
O5'
|
A:AMP501
|
3.9
|
32.2
|
1.0
|
O3P
|
A:AMP501
|
4.0
|
33.8
|
1.0
|
O
|
A:HOH639
|
4.0
|
32.4
|
1.0
|
C5'
|
A:AMP501
|
4.0
|
30.5
|
1.0
|
OD2
|
A:ASP249
|
4.1
|
32.9
|
1.0
|
OD1
|
A:ASP249
|
4.1
|
32.7
|
1.0
|
O
|
A:PHE151
|
4.1
|
29.3
|
1.0
|
CB
|
A:ASP150
|
4.4
|
31.3
|
1.0
|
O
|
A:HOH643
|
4.4
|
51.6
|
1.0
|
O
|
A:CYS245
|
4.5
|
34.7
|
1.0
|
CG
|
A:ASP249
|
4.5
|
32.0
|
1.0
|
O2P
|
A:AMP501
|
4.5
|
34.7
|
1.0
|
OD2
|
A:ASP312
|
4.6
|
33.9
|
1.0
|
CA
|
A:ASP150
|
4.6
|
29.8
|
1.0
|
C
|
A:ASP150
|
4.8
|
29.9
|
1.0
|
N
|
A:PHE151
|
4.8
|
29.3
|
1.0
|
|
Magnesium binding site 2 out
of 4 in 7lq0
Go back to
Magnesium Binding Sites List in 7lq0
Magnesium binding site 2 out
of 4 in the Crystal Structures and Ribonuclease Activity of the Flavivirus Host Factor ERI3 That Is Involved in Viral Rna Synthesis Define the Eri Subfamily of Structure-Specific 3-Prime - 5-Prime Exoribonucleases
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Crystal Structures and Ribonuclease Activity of the Flavivirus Host Factor ERI3 That Is Involved in Viral Rna Synthesis Define the Eri Subfamily of Structure-Specific 3-Prime - 5-Prime Exoribonucleases within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg503
b:45.9
occ:1.00
|
OE2
|
A:GLU152
|
2.1
|
32.8
|
1.0
|
OD2
|
A:ASP312
|
2.2
|
33.9
|
1.0
|
O1P
|
A:AMP501
|
2.3
|
34.2
|
1.0
|
OD2
|
A:ASP150
|
2.4
|
34.6
|
1.0
|
CG
|
A:ASP150
|
3.2
|
34.7
|
1.0
|
O2P
|
A:AMP501
|
3.2
|
34.7
|
1.0
|
CD
|
A:GLU152
|
3.2
|
31.4
|
1.0
|
O
|
A:PHE151
|
3.3
|
29.3
|
1.0
|
CG
|
A:ASP312
|
3.3
|
33.7
|
1.0
|
P
|
A:AMP501
|
3.3
|
34.5
|
1.0
|
MG
|
A:MG502
|
3.4
|
34.1
|
1.0
|
OE1
|
A:GLU152
|
3.7
|
31.1
|
1.0
|
CB
|
A:ASP312
|
3.7
|
32.3
|
1.0
|
OD1
|
A:ASP150
|
3.8
|
36.1
|
1.0
|
O
|
A:HOH628
|
3.9
|
37.9
|
1.0
|
O
|
A:HOH637
|
3.9
|
32.7
|
1.0
|
CB
|
A:ASP150
|
3.9
|
31.3
|
1.0
|
O
|
A:HOH643
|
4.0
|
51.6
|
1.0
|
O
|
A:ASP150
|
4.0
|
31.4
|
1.0
|
CA
|
A:GLY309
|
4.1
|
33.3
|
1.0
|
C
|
A:ASP150
|
4.2
|
29.9
|
1.0
|
C
|
A:PHE151
|
4.2
|
28.8
|
1.0
|
O3P
|
A:AMP501
|
4.3
|
33.8
|
1.0
|
OD1
|
A:ASP312
|
4.4
|
33.8
|
1.0
|
CG
|
A:GLU152
|
4.4
|
30.7
|
1.0
|
CA
|
A:HIS307
|
4.4
|
35.7
|
1.0
|
O5'
|
A:AMP501
|
4.5
|
32.2
|
1.0
|
O
|
A:SER308
|
4.5
|
34.6
|
1.0
|
N
|
A:GLY309
|
4.6
|
33.4
|
1.0
|
CA
|
A:ASP150
|
4.6
|
29.8
|
1.0
|
C5'
|
A:AMP501
|
4.6
|
30.5
|
1.0
|
C
|
A:SER308
|
4.7
|
33.9
|
1.0
|
C
|
A:HIS307
|
4.7
|
34.8
|
1.0
|
N
|
A:PHE151
|
4.7
|
29.3
|
1.0
|
N
|
A:GLU152
|
4.9
|
28.4
|
1.0
|
O
|
A:HOH679
|
4.9
|
35.3
|
1.0
|
O
|
A:HIS307
|
4.9
|
34.5
|
1.0
|
|
Magnesium binding site 3 out
of 4 in 7lq0
Go back to
Magnesium Binding Sites List in 7lq0
Magnesium binding site 3 out
of 4 in the Crystal Structures and Ribonuclease Activity of the Flavivirus Host Factor ERI3 That Is Involved in Viral Rna Synthesis Define the Eri Subfamily of Structure-Specific 3-Prime - 5-Prime Exoribonucleases
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Crystal Structures and Ribonuclease Activity of the Flavivirus Host Factor ERI3 That Is Involved in Viral Rna Synthesis Define the Eri Subfamily of Structure-Specific 3-Prime - 5-Prime Exoribonucleases within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg502
b:37.8
occ:1.00
|
O
|
B:HOH613
|
2.0
|
35.3
|
1.0
|
O3P
|
B:AMP501
|
2.0
|
35.7
|
1.0
|
O
|
B:HOH623
|
2.1
|
31.8
|
1.0
|
OD2
|
B:ASP150
|
2.1
|
34.1
|
1.0
|
O
|
B:HOH673
|
2.1
|
42.9
|
1.0
|
O
|
B:HOH624
|
2.2
|
34.5
|
1.0
|
CG
|
B:ASP150
|
3.1
|
33.6
|
1.0
|
P
|
B:AMP501
|
3.3
|
38.0
|
1.0
|
MG
|
B:MG503
|
3.4
|
40.1
|
1.0
|
OD1
|
B:ASP150
|
3.4
|
33.8
|
1.0
|
O1P
|
B:AMP501
|
3.9
|
36.9
|
1.0
|
O5'
|
B:AMP501
|
3.9
|
38.1
|
1.0
|
O
|
B:HOH636
|
4.0
|
40.1
|
1.0
|
OD1
|
B:ASP249
|
4.0
|
42.2
|
1.0
|
C5'
|
B:AMP501
|
4.1
|
39.2
|
1.0
|
OD2
|
B:ASP249
|
4.1
|
43.6
|
1.0
|
O
|
B:HOH637
|
4.1
|
41.3
|
1.0
|
O
|
B:PHE151
|
4.1
|
32.5
|
1.0
|
O
|
B:HOH643
|
4.2
|
53.5
|
1.0
|
O
|
B:CYS245
|
4.4
|
38.2
|
1.0
|
CB
|
B:ASP150
|
4.4
|
34.0
|
1.0
|
O2P
|
B:AMP501
|
4.5
|
36.8
|
1.0
|
CG
|
B:ASP249
|
4.5
|
42.8
|
1.0
|
OD2
|
B:ASP312
|
4.6
|
33.2
|
1.0
|
CA
|
B:ASP150
|
4.6
|
34.4
|
1.0
|
O
|
B:HOH609
|
4.7
|
47.8
|
1.0
|
N
|
B:PHE151
|
4.8
|
34.0
|
1.0
|
C
|
B:ASP150
|
4.8
|
34.4
|
1.0
|
|
Magnesium binding site 4 out
of 4 in 7lq0
Go back to
Magnesium Binding Sites List in 7lq0
Magnesium binding site 4 out
of 4 in the Crystal Structures and Ribonuclease Activity of the Flavivirus Host Factor ERI3 That Is Involved in Viral Rna Synthesis Define the Eri Subfamily of Structure-Specific 3-Prime - 5-Prime Exoribonucleases
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Crystal Structures and Ribonuclease Activity of the Flavivirus Host Factor ERI3 That Is Involved in Viral Rna Synthesis Define the Eri Subfamily of Structure-Specific 3-Prime - 5-Prime Exoribonucleases within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg503
b:40.1
occ:1.00
|
OE2
|
B:GLU152
|
2.1
|
34.0
|
1.0
|
O3P
|
B:AMP501
|
2.3
|
35.7
|
1.0
|
OD2
|
B:ASP312
|
2.3
|
33.2
|
1.0
|
OD2
|
B:ASP150
|
2.4
|
34.1
|
1.0
|
O
|
B:PHE151
|
3.1
|
32.5
|
1.0
|
CG
|
B:ASP150
|
3.1
|
33.6
|
1.0
|
CD
|
B:GLU152
|
3.2
|
34.0
|
1.0
|
O2P
|
B:AMP501
|
3.3
|
36.8
|
1.0
|
P
|
B:AMP501
|
3.3
|
38.0
|
1.0
|
CG
|
B:ASP312
|
3.4
|
31.6
|
1.0
|
MG
|
B:MG502
|
3.4
|
37.8
|
1.0
|
OE1
|
B:GLU152
|
3.7
|
34.9
|
1.0
|
O
|
B:ASP150
|
3.7
|
34.4
|
1.0
|
CB
|
B:ASP312
|
3.7
|
30.7
|
1.0
|
OD1
|
B:ASP150
|
3.7
|
33.8
|
1.0
|
CB
|
B:ASP150
|
3.8
|
34.0
|
1.0
|
O
|
B:HOH623
|
3.9
|
31.8
|
1.0
|
O
|
B:HOH637
|
3.9
|
41.3
|
1.0
|
C
|
B:PHE151
|
4.0
|
32.7
|
1.0
|
C
|
B:ASP150
|
4.0
|
34.4
|
1.0
|
O
|
B:HOH624
|
4.0
|
34.5
|
1.0
|
CA
|
B:GLY309
|
4.1
|
30.1
|
1.0
|
O1P
|
B:AMP501
|
4.3
|
36.9
|
1.0
|
CG
|
B:GLU152
|
4.3
|
32.3
|
1.0
|
CA
|
B:ASP150
|
4.4
|
34.4
|
1.0
|
OD1
|
B:ASP312
|
4.5
|
30.6
|
1.0
|
O5'
|
B:AMP501
|
4.5
|
38.1
|
1.0
|
N
|
B:PHE151
|
4.5
|
34.0
|
1.0
|
CA
|
B:HIS307
|
4.6
|
37.7
|
1.0
|
N
|
B:GLY309
|
4.6
|
30.7
|
1.0
|
C5'
|
B:AMP501
|
4.6
|
39.2
|
1.0
|
N
|
B:GLU152
|
4.7
|
31.6
|
1.0
|
O
|
B:SER308
|
4.7
|
33.2
|
1.0
|
C
|
B:HIS307
|
4.8
|
36.5
|
1.0
|
C
|
B:SER308
|
4.8
|
32.2
|
1.0
|
CA
|
B:PHE151
|
4.9
|
33.9
|
1.0
|
|
Reference:
R.Thapar,
A.S.Arvai,
J.A.Tainer.
Crystal Structures and Ribonuclease Activity of the Flavivirus Host Factor ERI3 That Is Involved in Viral Rna Synthesis Define the Eri Subfamily of Structure-Specific 3' - 5' Exoribonucleases To Be Published.
Page generated: Wed Oct 2 23:32:51 2024
|